tbuckley/cabot-search huggingface dataset:
Abstract LB261: The Akt-IWS1 signaling axis regulates microRNA activity
Authors: Niki Christodoulou, Maria Hatziapostolou, Cristina Montiel-Duarte, Elisabetta Verderio Edwards, Philip N. Tsichlis, Christos Polytarchou
Journal: Cancer Research (2023)

Abstract MicroRNAs are small single-stranded non-coding RNAs that regulate gene expression post-transcriptionally, by targeting the 3‘-untranslated region (3’-UTR) of mRNAs. The regulation of microRNAs at the transcriptional level is well-studied, however, how their activity is regulated remains largely elusive. The family of Akt serine/threonine protein kinases, comprised of Akt1, Akt2 and Akt3, regulates important cell functions including metabolism, survival, proliferation, and migration. We have previously shown that IWS1 (Interacts with Spt6), a factor involved in mRNA splicing and nuclear export, is phosphorylated specifically by Akt1 and Akt3 at Ser720/Thr721. Here, RNA extracts from NCI-H522 lung cancer cells, transduced with shIWS1 and reconstituted with wild type (Ser720/Thr721-IWS1) or phosphorylation-deficient IWS1 (Ala720/Ala721-IWS1) were subjected to RNA and microRNA sequencing. Bioinformatic analysis suggested that microRNAs expressed at similar levels in the two cell types have a different impact on their mRNA targets. microRNA activity reporter assays and western blot analysis for microRNA targets in these cells revealed increased microRNA activity in Ala720/Ala721-IWS1-expressing cells. Our findings were verified in a second cell line, the non-transformed immortalized colonic epithelial cells NCM460. microRNA activity reporter assays, western blot analyses and cell growth assays showed that microRNA effects are enhanced in cells expressing Ala720/Ala721-IWS1. Immunoprecipitation and proximity ligation assays showed that IWS1 interacts with proteins known to be associated with RISC, and this interaction is enhanced by Akt-mediated IWS1 phosphorylation. To evaluate the dependence of IWS1/RISC interaction on IWS1 phosphorylation, we employed Akt1− / −Akt2− / −Akt3− / − immortalized mouse lung fibroblasts, transduced with myc-Akt1 or myc-Akt2 or the empty retroviral vector. Immunoprecipitation experiments in these cells, before and after treatment with IGF1, revealed that IWS1 interacts with the RISC components specifically in Akt1-expressing cells upon Akt1 activation by IGF1. Overall, our data demonstrate that IWS1 interacts with RISC in a conserved Akt1-dependent manner and regulates the activity of microRNAs with significant effects on cellular properties. Citation Format: Niki Christodoulou, Maria Hatziapostolou, Cristina Montiel-Duarte, Elisabetta Verderio Edwards, Philip N. Tsichlis, Christos Polytarchou. The Akt-IWS1 signaling axis regulates microRNA activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB261.
Abstract LB258: Therapeutic advantage of targeting lysosome as signaling hub for metabolic conditions in malignant gliomas
Authors: Yongwei Jing, Masahiko Kobayashi, Atsushi Hirao
Journal: Cancer Research (2023)

Abstract Lysosome, as the digestive system of the cell, participated in numerous cell biological processes, such as macromolecular degradation, cell adhesion/migration, and apoptosis by regulating metabolic status and pro-growth signaling. Therefore, lysosome could be a promising therapeutic target for cancer therapy, but it remains unclear how lysosome is involved in cancer malignancy. In this study, to investigate the roles of function lysosomes in the regulation of malignant status, we evaluated the proteolytic activity of lysosomes using BODIPY-dye conjugated BSA (DQ-BSA) in malignant gliomas characterized by high aggressivity, destructivity, and invasiveness, glioblastoma multiforme (GBM). While most GBM patient-derived cells showed higher lysosomal proteolytic activity than an immortalized human neural progenitor cell line derived from the embryonic brain, levels of lysosome activity positively co-related with sphere formation. Multi-omics analysis demonstrated that the level of lysosomal proteolytic activity was co-related with metabolic status, including activated mitochondria biogenesis and amino acid transport. The orthotopic xenograft model revealed that lysosome activity in vitro is a critical biomarker representing malignant phenotypes of GBM. We found that the MiT/TFE family, a master regulator of lysosomal biogenesis, controlled the malignant progression of GBM, including therapy resistance, indicating that quality control of lysosomes is a critical determinant for the malignant properties of gliomas. To develop a novel therapeutic approach for targeting lysosomal function, we performed screening of FDA-approved compounds and found that lysosomotropic agents, which induced galectin-3 punctation as an indicator of lysosomal membrane damage, efficiently suppressed tumor growth. Ifenprodil, a clinically available drug that acts as a lysosomotropic agent, increased intracellular Ca2+ levels, resulting in mitochondrial reactive oxygen species-mediated cytotoxicity. Furthermore, we found that the efficacy of ifenprodil was remarkably enhanced by metabolic modifications, such as amino acid restriction, in vitro and in vivo. Collectively, these data indicate that lysosomes as signaling hubs for metabolic conditions play critical roles in the regulation of the malignant status of GBM patients. Our findings propose that lysosomal biogenesis is a promising target to develop a novel therapeutic approach for GBM. Citation Format: Yongwei Jing, Masahiko Kobayashi, Atsushi Hirao. Therapeutic advantage of targeting lysosome as signaling hub for metabolic conditions in malignant gliomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB258.
Abstract LB270: LINGO2-microRNA cluster controls oral cancer stemness ability and cancer progression
Authors: Wei-Min Chang, Li-Jie Li, Che-Hsuan Lin, Michael Hsiao, Peter Mu-Hsin Chang
Journal: Cancer Research (2023)

Abstract Cancer recurrence and metastasis are the primary reasons for treatment failure in late-stage oral cancer. Cancer stem cells are the root of cancer recurrence and metastasis. By using the microRNAome analysis of Taiwan OSCC cohort, we found miR-876-3p was highly correlated to OSCC recurrence. The precursor miR-876 promoted in vitro OSCC cell proliferation, migration, and cancer stemness and regulated several cancer stemness-relative genes such as NANOG, OCT4, and LIN28A expression. miR-876 and miR-873 are located in the second intron of the 5’-untransalation region (5’-UTR) at the alternative variant leucine-rich repeat and Ig domain containing 2 (LINGO2). Interestingly, only OSCC cells presented LINGO2 protein expression but did not show in primary oral keratinocytes (HOK). The unique CpG islands at the alternative transcription start site of LINGO2 hinted at crucial epigenetic regulation that controls LINGO2 activation. Silencing of LINGO2 expression reduced OSCC cell growth and cancer stemness abilities. LINGO2 expression was higher in OSCC tumor tissue than in adjacent normal tissue in both Taiwan and The Cancer Genome Atlas (TCGA) head and neck cancer cohorts. Moreover, LINGO2 also served as a poor prognostic marker in cancer patients' overall and recurrent free survival time. In summary, we found a novel LINGO2-microRNA cluster that regulates OSCC stemness and metastasis abilities. Those cancer specific expressions may provide a new therapy niche in OSCC cancer therapy. Citation Format: Wei-Min Chang, Li-Jie Li, Che-Hsuan Lin, Michael Hsiao, Peter Mu-Hsin Chang. LINGO2-microRNA cluster controls oral cancer stemness ability and cancer progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB270.
Abstract LB259: Distinct microRNA signature and suppression of ZFP36L1 define ASCL1-positive lung adenocarcinoma
Authors: Naoya Miyashita, Takayoshi Enokido, Masafumi Horie, Hiroshi I. Suzuki, Rei Matsuki, Hans Brunnström, Patrick Micke, Takahide Nagase, Akira Saito
Journal: Cancer Research (2023)

Abstract Background: Achaete-scute family bHLH transcription factor 1 (ASCL1) is a master transcription factor involved in neuroendocrine differentiation. ASCL1 is expressed in approximately 10% of lung adenocarcinomas and exerts tumor-promoting effects. However, microRNA (miRNA) profiles regulated by ASCL1 in lung adenocarcinoma cells remain unexplored. Method: We analyzed public database of gene expression profiling (RNA-sequencing and miRNA expression data). We also studied miRNA profiles in ASCL1-positive lung adenocarcinoma cells and identified a subset of miRNAs downregulated by ASCL1 knockdown. We examined functions of genes suppressed by miRNAs in ASCL1-positive lung adenocarcinoma cell line, VMRC-LCD. Result: We identified miRNA profiles in ASCL1-positive lung adenocarcinomas and found several miRNAs closely associated with ASCL1 expression, including miR-375, miR-95-3p/miR-95-5p, miR-124-3p, and members of the miR-17~92 family. Similar to small cell lung cancer, Yes1 associated transcriptional regulator (YAP1), a representative miR-375 target gene, is suppressed in ASCL1-positive lung adenocarcinomas. ASCL1 knockdown followed by miRNA profiling in a cell culture model further revealed that ASCL1 positively regulates miR-124-3p and members of the miR-17~92 family. Integrative transcriptomic analyses identified the RNA-binding protein zinc finger protein 36 like 1 (ZFP36L1) as a target gene of miR-124-3p, and immunohistochemical studies have demonstrated that ASCL1-positive lung adenocarcinomas are associated with low ZFP36L1 protein levels. Cell culture studies have shown that ectopic ZFP36L1 expression inhibits cell proliferation, survival, and cell cycle progression. Mechanistically, ZFP36L1 negatively regulated tumorigenic genes, including E2F transcription factor 1 (E2F1) and snail family transcriptional repressor 1 (SNAI1), indicating a tumor-suppressing action. Conclusion: Our study revealed that suppression of ZFP36L1 via ASCL1-regulated miR-124-3p could induce tumor-promoting effects, providing evidence that ASCL1-mediated regulation of miRNAs shapes malignant features of ASCL1-positive lung adenocarcinomas. Citation Format: Naoya Miyashita, Takayoshi Enokido, Masafumi Horie, Hiroshi I. Suzuki, Rei Matsuki, Hans Brunnström, Patrick Micke, Takahide Nagase, Akira Saito. Distinct microRNA signature and suppression of ZFP36L1 define ASCL1-positive lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB259.
Abstract LB096: IL15-engineered tumor infiltrating lymphocytes (cytoTIL15TM) exhibit activity against autologous tumor cells from multiple solid tumor indications without IL2
Authors: Kyle D. Pedro, Rachel Burga, Alonso Villasmil Ocando, Meghan Langley, Gauri Kulkarni, Zheng Ao, Benjamin Primack, Theresa Ross, Violet Young, Jeremy Tchaicha, Michelle Ols, Jan Ter Meulen
Journal: Cancer Research (2023)

Abstract Tumor infiltrating lymphocyte (TIL) therapy has shown promising results in the treatment of metastatic melanoma. However, TIL therapy has conventionally required co-administration of IL2, which is associated with toxicity in patients. We previously showed that melanoma TILs engineered to express membrane-bound IL15 (mbIL15) under the control of the ligand acetazolamide (ACZ) can achieve IL2-independent expansion during manufacturing, antigen-independent persistence in vitro and anti-tumor efficacy in vivo. In the current study, we extend the cytoTIL15 cell therapy product concept to indications beyond melanoma including non-small cell lung cancers (NSCLC), triple-negative breast cancers (TNBC) and head and neck squamous cell carcinomas (HNSCC), tumor types which represent significant unmet medical needs, particularly in the post-checkpoint inhibitor refractory setting. TILs from primary NSCLC, HNSCC and TNBC were engineered to express mbIL15 in the presence of ACZ and expanded in the absence of IL2 using our proprietary rapid expansion protocol (REP). CytoTIL15 cells were predominantly CD8 positive, enriched for mbIL15 expression and maintained T cell receptor variable beta chain (TCRVβ) diversity throughout expansion. In vitro antigen- and cytokine-independent survival and polyfunctionality of cytoTIL15 cells was measured from cultures that included ACZ. To assess anti-tumor activity, cytoTIL15 cells were co-cultured with autologous patient-derived cell lines (PDc) or tumor digests from patient-derived xenografts (PDx), and cytotoxicity and IFNγ release into supernatant was measured. In vitro, cytoTIL15 cells + ACZ exhibited similar or increased polyfunctionality compared to unengineered TIL + IL2. Unlike unengineered TILs, cytoTIL15 cells + ACZ persisted in an antigen-free setting without IL2, were cytotoxic to autologous PDc and released IFNγ in response to autologous PDx tumor digest. Taken together, these data show that IL2-independent, fully functional cytoTIL15 cells can successfully be generated from tumors such as NSCLC, HNSCC &amp; TNBC, which afflict large numbers of patients. Citation Format: Kyle D. Pedro, Rachel Burga, Alonso Villasmil Ocando, Meghan Langley, Gauri Kulkarni, Zheng Ao, Benjamin Primack, Theresa Ross, Violet Young, Jeremy Tchaicha, Michelle Ols, Jan Ter Meulen. IL15-engineered tumor infiltrating lymphocytes (cytoTIL15TM) exhibit activity against autologous tumor cells from multiple solid tumor indications without IL2 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB096.
Abstract LB269: Inhibition Of C-C chemokine receptor 7 extends survival rate in murine model of T-cell acute lymphoblastic leukemia
Authors: Anahi Sanchez, Aaron E. Vazquez, Janet M. Valenzuela, Savannah Stanley, Colin A. Bill, Charlotte M. Vines
Journal: Cancer Research (2023)

Abstract C-C Chemokine Receptor 7 (CCR7) expression in pediatric T-cell acute lymphoblastic leukemia (T-ALL) promotes entry of leukemic cells into the central nervous system (CNS), where the disease finds sanctuary from systemic chemotherapies. To confirm that Notch1 drives expression of CCR7, we modified the ROSA26-PRDM14 ([PRDI-BF1 (positive regulatory domain I-binding factor 1) and RIZ (retinoblastoma interacting zinc finger) homology domain containing 14]) MX-1 Cre inducible CD8+ T-ALL mouse model. This model, upon induction with polyI:C, expresses NOTCH1 downstream of PRDM14, and the T-ALL cells enter the CNS during leukemogenesis. We crossed these mice with ROSA26-Luc2 mice, which allows for tracking of T-ALL cells during disease progression. We questioned if these T-ALL cells expressed CCR7. We found that not only do the T-ALL cells express CCR7 and enter the CNS, but that a CCR7 antagonist, CCL198-83 administered during leukemogenesis doubles the mean survival of the CCL198-83 treated mice from 45 to 90 days. These studies provide a novel platform for a potential therapeutic that can be used to limit CNS entry and potentially recycling through the CNS. Citation Format: Anahi Sanchez, Aaron E. Vazquez, Janet M. Valenzuela, Savannah Stanley, Colin A. Bill, Charlotte M. Vines. Inhibition Of C-C chemokine receptor 7 extends survival rate in murine model of T-cell acute lymphoblastic leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB269.
Abstract LB075: Cancers adapt to their mutational load by buffering protein misfolding stress
Authors: Susanne Tilk, Judith Frydman, Dmitri Petrov, Christina Curtis
Journal: Cancer Research (2023)

Abstract In asexual populations that don’t undergo recombination, such as cancer, deleterious mutations are expected to accrue readily due to genome-wide linkage between mutations. Despite this mutational load of often thousands of deleterious mutations, many tumors thrive. How tumors survive the damaging consequences of this mutational load is not well understood. Here, we investigate the functional consequences of mutational load in 10,295 human tumors by quantifying their phenotypic response through changes in gene expression. Using a generalized linear mixed model (GLMM), we find that high mutational load tumors up-regulate proteostasis machinery related to the mitigation and prevention of protein misfolding. We replicate these expression responses in cancer cell lines and show that the viability in high mutational load cancer cells is strongly dependent on complexes that degrade and refold proteins. This indicates that upregulation of proteostasis machinery is causally important for high mutational burden tumors and uncovers new therapeutic vulnerabilities. Citation Format: Susanne Tilk, Judith Frydman, Dmitri Petrov, Christina Curtis. Cancers adapt to their mutational load by buffering protein misfolding stress [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB075.
Abstract LB354: 9p arm loss is an important predictor of immune evasion in several human cancers
Authors: Joy Bianchi
Journal: Cancer Research (2023)

Abstract The identification of biomarkers that predict patient response to immune checkpoint blockade (ICB) is a key focus of current cancer research. We and others have found that high levels of Somatic Copy Number Alterations (SCNAs) in tumors are associated with decreased infiltration by cytotoxic immune cells and predict patient’s response to ICB. Recently, we predicted that the strongest SCNA driver of cytotoxic T cell depletion in HPV-negative oral cancer, was the loss of the entire 9p arm and that it was a marker of poor survival in recurrent oral cancers treated by anti-PD1 therapy. 9p arm loss is among the most common SCNAs in solid tumors and we revealed its importance beyond 9p21.3 deletion (i.e., CDKN2A and the IFNA cluster).To systematically investigate the immune-related role of 9p deletion and other SCNAs in cancer, we have developed a computational pipeline to identify the genes altered by SCNAs predicting the strongest risk of cancer immune evasion. We analyzed 7 solid tumor types and identified thousands of tumor-specific SCNAs predicting an immune cold phenotype but only ~100 SCNAs were conserved across all tumor types. Strikingly, 60% of the conserved deletions were localized on the 9p arm and the strongest 9p candidates included some known cancer drivers but also new candidates such as RANBP6 and TOPORS, that have been suggested to decrease proinflammatory and pro-immunogenic molecules. We have identified a 17-gene cluster deletion in 9p13 composed mostly of genes involved in proteasomal degradation or membrane trafficking, suggesting that its deletion might disturb MHC-mediated antigen presentation. We are now engineering human and mouse oral cancer cell lines to recapitulate 9p deletion and decipher its role in immune evasion through in vitro and in vivo immunological assays. We are also using the parameters we determined in our computational pipeline to develop a machine learning method improving our prediction of SCNAs driving immune evasion. Our findings identified 9p deletion as a novel biomarker for predicting clinical benefit of ICB and will allow a better understanding of the SCNA-mediated mechanisms suppressing tumor immune response. Citation Format: Joy Bianchi. 9p arm loss is an important predictor of immune evasion in several human cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB354.
Abstract LB179: Automated viable circulating tumor cell (CTC) isolation enables efficient single-cell multi-omics analysis in a clinical setting
Authors: Janet Dickerson, Dylan Dufek, Robbie Huff, Stephenie Jones, Jennifer Barber-Singh, Christopher Brandt, Judy Muller-Cohn, Rolf Muller, Yipeng Wang
Journal: Cancer Research (2023)

Abstract Circulating tumor cells (CTCs) are rare cells found in peripheral blood or other body fluids of cancer patients. Single-cell multi-omics analysis of CTCs can provide critical information and insights for tumor heterogeneity, early detection, residual disease, recurrence, and response and resistance to therapies. However, the adoption of single cell analysis in a clinical setting has been challenging due to complicated and lengthy workflows, lack of automation, low throughput, cell loss, inefficient cell picking, and nucleic acid degradation. To overcome these challenges, we have developed the fully automated LiquidScan liquid biopsy platform as a solution for CTC enrichment and single cell isolation. Whole blood samples were collected from breast, prostate, and lung cancer patients using BioFluidica blood collection tubes. CTCs were enriched with LiquidScan platform coupled with microfluidic affinity selection of rare cells with antibodies against cancer specific surface markers. Cell eluates released from microfluidic chips were further sorted and individual cells were placed into individual wells of PCR plates. The isolated single cells were processed with either whole genome amplification for DNA analysis or pre-amplification of RNA for transcriptome profiling. Cell viability and RNA integrity were assessed for enriched cells post LiquidScan processing. Whole blood samples were directly loaded to microfluidic chips and processed (capture, wash, release and elute) using Hamilton robot for automated processing with no require to red blood cell lysis. The sample processing time was approximately 3 hours with up to 8 samples processed simultaneously. Enriched cells were 70% viable on average post LiquidScan sample processing. The RNA RIN score for the enriched cells was 6 on average. Success rate of DNA amplifications and RNA pre-Amplifications were both over 90% across all samples processed. The LiquidScan platform provides a solution for fast, automated single viable cell isolation making downstream molecular analysis possible in a clinical setting. Protocols for RNA pre-amplification and DNA sequencing including copy number analysis and targeted resequencing have been developed. Single cell DNA methylation and proteomics assay development is in progress. Citation Format: Janet Dickerson, Dylan Dufek, Robbie Huff, Stephenie Jones, Jennifer Barber-Singh, Christopher Brandt, Judy Muller-Cohn, Rolf Muller, Yipeng Wang. Automated viable circulating tumor cell (CTC) isolation enables efficient single-cell multi-omics analysis in a clinical setting [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB179.